scholarly journals The Distribution of Fitness Effects Among Beneficial Mutations

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1519-1526 ◽  
Author(s):  
H Allen Orr

AbstractWe know little about the distribution of fitness effects among new beneficial mutations, a problem that partly reflects the rarity of these changes. Surprisingly, though, population genetic theory allows us to predict what this distribution should look like under fairly general assumptions. Using extreme value theory, I derive this distribution and show that it has two unexpected properties. First, the distribution of beneficial fitness effects at a gene is exponential. Second, the distribution of beneficial effects at a gene has the same mean regardless of the fitness of the present wild-type allele. Adaptation from new mutations is thus characterized by a kind of invariance: natural selection chooses from the same spectrum of beneficial effects at a locus independent of the fitness rank of the present wild type. I show that these findings are reasonably robust to deviations from several assumptions. I further show that one can back calculate the mean size of new beneficial mutations from the observed mean size of fixed beneficial mutations.

2020 ◽  
Author(s):  
Aida Alonso-del Valle ◽  
Ricardo León-Sampedro ◽  
Jerónimo Rodríguez-Beltrán ◽  
Javier DelaFuente ◽  
Marta Hernández-García ◽  
...  

Introductory paragraphPlasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the distribution of fitness effects (DFE) for the major antibiotic resistance plasmid pOXA-48 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48 produced an overall reduction in bacterial fitness, the DFE was dominated by quasi-neutral effects, and beneficial effects were observed in several isolates. Incorporating these data into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. Moreover, genomic results showed a link between plasmid fitness effects and bacterial phylogeny, helping to explain pOXA-48 epidemiology. Our results provide a simple and general explanation for plasmid persistence in natural bacterial communities.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 541-541
Author(s):  
Veronica H. Flood ◽  
Carol A. Lederman ◽  
Jeffrey S. Wren ◽  
Pamela A. Christopherson ◽  
Kenneth D. Friedman ◽  
...  

Abstract Abstract 541 Von Willebrand factor (VWF) plays a key role in coagulation by tethering platelets to injured subendothelium through binding sites for collagen and platelet GPIb. Laboratory testing for von Willebrand disease (VWD) utilizes various assays of VWF protein and function, but collagen binding (VWF:CB) has not always been performed. Samples obtained from a large, multi-center US study of von Willebrand disease (VWD), the Zimmerman Program for the Molecular and Clinical Biology of VWD (ZPMCB-VWD), were evaluated for VWF:CB. Whole blood was collected for DNA sequencing and plasma samples were collected for VWF testing. VWF antigen (VWF:Ag), ristocetin cofactor activity (VWF:RCo), and VWF:CB were performed in the BloodCenter of Wisconsin hemostasis laboratory. A normal range for the VWF:CB was established using 233 healthy controls enrolled in the ZPMCB-VWD. The mean VWF:Ag was 105 IU/dL and the mean VWF:CB was 123 U/dL, with a mean VWF:CB/VWF:Ag ratio of 1.19. This yields a normal range of 0.86-1.51 (mean ± 2 SD). No sequence variations in the VWF A3 domain affecting VWF:CB were observed in the healthy controls. Collagen binding was then examined in subjects enrolled with a diagnosis of VWD. The index case in one family was noted to have a low VWF:CB/VWF:Ag ratio of 0.54. The VWF:Ag was 41 IU/dL, VWF:RCo was 44 IU/dL, VWF:CB was 22 U/dL, and multimer distribution was normal. Decreased VWF:CB/VWF:Ag was found in the father and sister of the index case, while the mother had normal VWF:CB/VWF:Ag. The index case initially presented with epistaxis and easy bruising. Her bleeding score was 8, as determined by the revised European Union questionnaire. DNA sequencing of exons 28-32 was performed and revealed a heterozygous mutation (5356C>G) predicting replacement of wild-type histidine 1786 by aspartic acid in all affected family members. This amino acid is located in a critical face of the A3 loop. The 1786D mutation was cloned into a full-length VWF expression vector and expressed, as was a previously reported collagen-binding mutation, 1731T. Collagen binding assays were performed using type I human placental collagen at 5 μg/mL or type III human placental collagen at 1 μg/mL to capture either plasma or recombinant VWF (rVWF). Both mutations had normal expression, at 97% and 87% of the expression seen with wild-type VWF, respectively. Multimer distribution was also normal, including presence of high molecular weight multimers. Plasma from family members heterozygous for the H1786D mutation showed a mean VWF:CB/VWF:Ag ratio of 0.23 ± 0.05 (mean ± SD) for type I collagen and 0.50 ± 0.11 for type III collagen. When the rVWF constructs were examined, the novel 1786D mutation showed essentially no binding to either type I or type III collagen, at <1% of wild-type rVWF. In contrast, the previously reported collagen binding mutation 1731T showed VWF:CB/VWF:Ag ratios of 45% for type I and 50% for type III collagen when compared to wild-type rVWF. As the proband had a minimally decreased VWF:Ag, we then examined collagen binding in ZPMCB-VWD subjects with VWF:Ag between 30 and 50 IU/dL. The mean VWF:CB/VWF:Ag ratio in this group was 1.02, with a range of 0.62 to 1.28. These results, taken together with the data in the healthy controls, suggest that decreased VWF:CB/VWF:Ag ratios may identify a specific defect in VWF function. In particular, the H1786D mutation appears to result in a complete loss of VWF's ability to bind either type I or type III collagen. The subjects with this mutation were all heterozygous, which may account for reduction, rather than absence, of in vitro VWF:CB. The VWF:CB may be useful in diagnosis of VWD, and a decreased VWF:CB/VWF:Ag ratio in the face of normal VWF multimer distribution may reflect specific loss of collagen binding ability leading to bleeding symptoms. Disclosures: Montgomery: GTI Diagnostics: Consultancy; Baxter: Consultancy; AstraZeneca: Consultancy; Bayer: Research Funding; CSL Behring: Membership on an entity's Board of Directors or advisory committees.


2020 ◽  
Vol 10 (7) ◽  
pp. 2317-2326 ◽  
Author(s):  
Tom R. Booker

Characterizing the distribution of fitness effects (DFE) for new mutations is central in evolutionary genetics. Analysis of molecular data under the McDonald-Kreitman test has suggested that adaptive substitutions make a substantial contribution to between-species divergence. Methods have been proposed to estimate the parameters of the distribution of fitness effects for positively selected mutations from the unfolded site frequency spectrum (uSFS). Such methods perform well when beneficial mutations are mildly selected and frequent. However, when beneficial mutations are strongly selected and rare, they may make little contribution to standing variation and will thus be difficult to detect from the uSFS. In this study, I analyze uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. As expected, frequent, mildly beneficial mutations contribute substantially to standing genetic variation and parameters are accurately recovered from the uSFS. However, when advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contribution adaptive mutations make to molecular evolution. Fortunately, the parameters for the distribution of fitness effects for harmful mutations are estimated with high accuracy and precision. The results from this study suggest that the parameters of positively selected mutations obtained by analysis of the uSFS should be treated with caution and that variability at linked sites should be used in conjunction with standing variability to estimate parameters of the distribution of fitness effects in the future.


1999 ◽  
Vol 87 (5) ◽  
pp. 1776-1785 ◽  
Author(s):  
Y. Ohira ◽  
T. Yoshinaga ◽  
M. Ohara ◽  
I. Nonaka ◽  
T. Yoshioka ◽  
...  

After 2 or 4 mo of bed rest (6° head-down tilt) and 1 mo of ambulation, there was a tendency toward a higher percentage of fibers expressing fast myosin heavy chain (MHC) isoforms and a de novo appearance of fibers coexpressing type I+IIa+IIx and IIa+IIx MHC in human soleus fibers. After 2 and 4 mo of bed rest, the mean size of type I fibers decreased by 12 ( P > 0.05) and 39%, respectively. Because myonuclear number/mm of fiber length was unchanged, myonuclear domain was smaller after bed rest than before. The mean size and myonuclear domain of type I fibers were largest after 1 mo of recovery. The effects of wearing an antigravity device (Penguin suit), which had a modest but continuous resistance at the knee and ankle (Penguin-1) or knee resistance without loading on the ankle (Penguin-2), for 10 consecutive h/day were determined during 2 mo of bed rest. Mean fiber sizes in Penguin-1, but not Penguin-2, group were maintained at or above pre-bed-rest levels, whereas neither group showed phenotype changes. Myonuclear domain in type I fibers was larger in Penguin-1 and smaller in Penguin-2 group post- compared with pre-bed rest, indicating that a single daily 10-h bout of modest muscle loading can prevent bed-rest-induced soleus fiber atrophy but has minimal effect on myosin phenotype. The specific adaptive cellular strategies involved may be a function of the duration and magnitude of the adaptive stimulus as well as the immediate activity history of the fiber before the newly changed functional demands.


Nutrients ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1482
Author(s):  
Shasika Jayarathne ◽  
Latha Ramalingam ◽  
Hunter Edwards ◽  
Siva A. Vanapalli ◽  
Naima Moustaid-Moussa

Aging and healthspan are determined by both environmental and genetic factors. The insulin/insulin-like growth factor-1(IGF-1) pathway is a key mediator of aging in Caenorhabditis elegans and mammals. Specifically, DAF-2 signaling, an ortholog of human IGF, controls DAF-16/FOXO transcription factor, a master regulator of metabolism and longevity. Moreover, mitochondrial dysfunction and oxidative stress are both linked to aging. We propose that daily supplementation of tart cherry extract (TCE), rich in anthocyanins with antioxidant properties may exert dual benefits for mitochondrial function and oxidative stress, resulting in beneficial effects on aging in C. elegans. We found that TCE supplementation at 6 μg or 12 μg/mL, increased (p < 0.05) the mean lifespan of wild type N2 worms, respectively, when compared to untreated control worms. Consistent with these findings, TCE upregulated (p < 0.05) expression of longevity-related genes such as daf-16 and aak-2 (but not daf-2 or akt-1 genes) and genes related to oxidative stress such as sod-2. Further, we showed that TCE supplementation increased spare respiration in N2 worms. However, TCE did not change the mean lifespan of daf-16 and aak-2 mutant worms. In conclusion, our findings indicate that TCE confers healthspan benefits in C. elegans through enhanced mitochondrial function and reduced oxidative stress, mainly via the DAF-16 pathway.


2019 ◽  
Author(s):  
Tom R. Booker

AbstractCharacterising the distribution of fitness effects (DFE) for new mutations is central in evolutionary genetics. Analysis of molecular data under the McDonald-Kreitman test has suggested that adaptive substitutions make a substantial contribution to between-species divergence. Methods have been proposed to estimate the parameters of the distribution of fitness effects for positively selected mutations from the unfolded site frequency spectrum (uSFS). However, when beneficial mutations are strongly selected and rare, they may make little contribution to standing variation and will thus be difficult to detect from the uSFS. In this study, I analyse uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. When advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contribution adaptive mutations make to molecular evolution. Fortunately, the parameters for the distribution of fitness effects for harmful mutations are estimated with high accuracy and precision. The results from this study suggest that the parameters of positively selected mutations obtained by analysis of the uSFS should be treated with caution and that variability at linked sites should be used in conjunction with standing variability to estimate parameters of the distribution of fitness effects in the future.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aida Alonso-del Valle ◽  
Ricardo León-Sampedro ◽  
Jerónimo Rodríguez-Beltrán ◽  
Javier DelaFuente ◽  
Marta Hernández-García ◽  
...  

AbstractPlasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.


2018 ◽  
Vol 4 (4) ◽  
pp. 519-522
Author(s):  
Jeyakumar S ◽  
Jagatheesan Alagesan ◽  
T.S. Muthukumar

Background: Frozen shoulder is disorder of the connective tissue that limits the normal Range of motion of the shoulder in diabetes, frozen shoulder is thought to be caused by changes to the collagen in the shoulder joint as a result of long term Hypoglycemia. Mobilization is a therapeutic movement of the joint. The goal is to restore normal joint motion and rhythm. The use of mobilization with movement for peripheral joints was developed by mulligan. This technique combines a sustained application of manual technique “gliding” force to the joint with concurrent physiologic motion of joint, either actively or passively. This study aims to find out the effects of mobilization with movement and end range mobilization in frozen shoulder in Type I diabetics. Materials and Methods: 30 subjects both male and female, suffering with shoulder pain and clinically diagnosed with frozen shoulder was recruited for the study and divided into two groups with 15 patients each based on convenient sampling method. Group A patients received mobilization with movement and Group B patients received end range mobilization for three weeks. The outcome measurements were SPADI, Functional hand to back scale, abduction range of motion using goniometer and VAS. Results: The mean values of all parameters showed significant differences in group A as compared to group B in terms of decreased pain, increased abduction range and other outcome measures. Conclusion: Based on the results it has been concluded that treating the type 1 diabetic patient with frozen shoulder, mobilization with movement exercise shows better results than end range mobilization in reducing pain and increase functional activities and mobility in frozen shoulder.


2015 ◽  
Vol 24 (4) ◽  
pp. 523-526 ◽  
Author(s):  
Yoshihiro Maruo ◽  
Mahdiyeh Behnam ◽  
Shinichi Ikushiro ◽  
Sayuri Nakahara ◽  
Narges Nouri ◽  
...  

Background: Crigler–Najjar syndrome type I (CN-1) and type II (CN-2) are rare hereditary unconjugated hyperbilirubinemia disorders. However, there have been no reports regarding the co-existence of CN-1 and CN-2 in one family. We experienced a case of an Iranian family that included members with either CN-1 or CN-2. Genetic analysis revealed a mutation in the bilirubin UDP-glucuronosyltransferase (UGT1A1) gene that resulted in residual enzymatic activity.Case report: The female proband developed severe hyperbilirubinemia [total serum bilirubin concentration (TB) = 34.8 mg/dL] with bilirubin encephalopathy (kernicterus) and died after liver transplantation. Her family history included a cousin with kernicterus (TB = 30.0 mg/dL) diagnosed as CN-1. Her great grandfather (TB unknown) and uncle (TB = 23.0 mg/dL) developed jaundice, but without any treatment, they remained healthy as CN-2. Results: The affected cousin was homozygous for a novel frameshift mutation (c.381insGG, p.C127WfsX23). The affected uncle was compound heterozygous for p.C127WfsX23 and p.V225G linked with A(TA)7TAA. p.V225G-UGT1A1 reduced glucuronidation activity to 60% of wild-type. Thus, linkage of A(TA)7TAA and p.V225G might reduce UGT1A1 activity to 18%–36 % of the wild-type. Conclusion: Genetic and in vitro expression analyses are useful for accurate genetic counseling for a family with a history of both CN-1 and CN-2. Abbreviations: CN-1: Crigler–Najjar syndrome type I; CN-2: Crigler–Najjar syndrome type II; GS: Gilbert syndrome; UGT1A1: bilirubin UDP-glucuronosyltransferase; WT: Wild type; TB: total serum bilirubin.


2020 ◽  
Vol 26 (1) ◽  
pp. 53-59 ◽  
Author(s):  
Jennifer M. Strahle ◽  
Rukayat Taiwo ◽  
Christine Averill ◽  
James Torner ◽  
Jordan I. Gewirtz ◽  
...  

OBJECTIVEIn patients with Chiari malformation type I (CM-I) and a syrinx who also have scoliosis, clinical and radiological predictors of curve regression after posterior fossa decompression are not well known. Prior reports indicate that age younger than 10 years and a curve magnitude < 35° are favorable predictors of curve regression following surgery. The aim of this study was to determine baseline radiological factors, including craniocervical junction alignment, that might predict curve stability or improvement after posterior fossa decompression.METHODSA large multicenter retrospective and prospective registry of pediatric patients with CM-I (tonsils ≥ 5 mm below the foramen magnum) and a syrinx (≥ 3 mm in width) was reviewed for clinical and radiological characteristics of CM-I, syrinx, and scoliosis (coronal curve ≥ 10°) in patients who underwent posterior fossa decompression and who also had follow-up imaging.RESULTSOf 825 patients with CM-I and a syrinx, 251 (30.4%) were noted to have scoliosis present at the time of diagnosis. Forty-one (16.3%) of these patients underwent posterior fossa decompression and had follow-up imaging to assess for scoliosis. Twenty-three patients (56%) were female, the mean age at time of CM-I decompression was 10.0 years, and the mean follow-up duration was 1.3 years. Nine patients (22%) had stable curves, 16 (39%) showed improvement (> 5°), and 16 (39%) displayed curve progression (> 5°) during the follow-up period. Younger age at the time of decompression was associated with improvement in curve magnitude; for those with curves of ≤ 35°, 17% of patients younger than 10 years of age had curve progression compared with 64% of those 10 years of age or older (p = 0.008). There was no difference by age for those with curves > 35°. Tonsil position, baseline syrinx dimensions, and change in syrinx size were not associated with the change in curve magnitude. There was no difference in progression after surgery in patients who were also treated with a brace compared to those who were not treated with a brace for scoliosis.CONCLUSIONSIn this cohort of patients with CM-I, a syrinx, and scoliosis, younger age at the time of decompression was associated with improvement in curve magnitude following surgery, especially in patients younger than 10 years of age with curves of ≤ 35°. Baseline tonsil position, syrinx dimensions, frontooccipital horn ratio, and craniocervical junction morphology were not associated with changes in curve magnitude after surgery.


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